Merge pull request #70 from DanielaSchacherer/pathology_notebook_update

ENH: added new introductory notebook
ImagingDataCommons · Aug 15, 2024 · e2c64ad · e2c64ad
2 parents 94b888c + aded996
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diff --git a/...books/pathomics/idc_pathomics/__init__.py → ...ooks/deprecated/idc_pathomics/__init__.py b/...books/pathomics/idc_pathomics/__init__.py → ...ooks/deprecated/idc_pathomics/__init__.py
diff --git a/.../pathomics/idc_pathomics/data/__init__.py → ...deprecated/idc_pathomics/data/__init__.py b/.../pathomics/idc_pathomics/data/__init__.py → ...deprecated/idc_pathomics/data/__init__.py
diff --git a/...athomics/idc_pathomics/data/data_point.py → ...precated/idc_pathomics/data/data_point.py b/...athomics/idc_pathomics/data/data_point.py → ...precated/idc_pathomics/data/data_point.py
diff --git a/.../pathomics/idc_pathomics/data/data_set.py → ...deprecated/idc_pathomics/data/data_set.py b/.../pathomics/idc_pathomics/data/data_set.py → ...deprecated/idc_pathomics/data/data_set.py
diff --git a/...ics/idc_pathomics/data/tile_generation.py → ...ted/idc_pathomics/data/tile_generation.py b/...ics/idc_pathomics/data/tile_generation.py → ...ted/idc_pathomics/data/tile_generation.py
diff --git a/...homics/idc_pathomics/data/tile_sorting.py → ...ecated/idc_pathomics/data/tile_sorting.py b/...homics/idc_pathomics/data/tile_sorting.py → ...ecated/idc_pathomics/data/tile_sorting.py
diff --git a/...oks/pathomics/idc_pathomics/data/utils.py → ...ks/deprecated/idc_pathomics/data/utils.py b/...oks/pathomics/idc_pathomics/data/utils.py → ...ks/deprecated/idc_pathomics/data/utils.py
diff --git a/...mics/idc_pathomics/evaluation/__init__.py → ...ated/idc_pathomics/evaluation/__init__.py b/...mics/idc_pathomics/evaluation/__init__.py → ...ated/idc_pathomics/evaluation/__init__.py
diff --git a/...omics/idc_pathomics/evaluation/heatmap.py → ...cated/idc_pathomics/evaluation/heatmap.py b/...omics/idc_pathomics/evaluation/heatmap.py → ...cated/idc_pathomics/evaluation/heatmap.py
diff --git a/...s/idc_pathomics/evaluation/predictions.py → ...d/idc_pathomics/evaluation/predictions.py b/...s/idc_pathomics/evaluation/predictions.py → ...d/idc_pathomics/evaluation/predictions.py
diff --git a/...pathomics/idc_pathomics/evaluation/roc.py → ...eprecated/idc_pathomics/evaluation/roc.py b/...pathomics/idc_pathomics/evaluation/roc.py → ...eprecated/idc_pathomics/evaluation/roc.py
diff --git a/...pathomics/idc_pathomics/model/__init__.py → ...eprecated/idc_pathomics/model/__init__.py b/...pathomics/idc_pathomics/model/__init__.py → ...eprecated/idc_pathomics/model/__init__.py
diff --git a/...thomics/idc_pathomics/model/base_model.py → ...recated/idc_pathomics/model/base_model.py b/...thomics/idc_pathomics/model/base_model.py → ...recated/idc_pathomics/model/base_model.py
diff --git a/.../idc_pathomics/model/inceptionv3_model.py → .../idc_pathomics/model/inceptionv3_model.py b/.../idc_pathomics/model/inceptionv3_model.py → .../idc_pathomics/model/inceptionv3_model.py
diff --git a/...s/idc_pathomics/tissue_type_data_TCIA.csv → ...d/idc_pathomics/tissue_type_data_TCIA.csv b/...s/idc_pathomics/tissue_type_data_TCIA.csv → ...d/idc_pathomics/tissue_type_data_TCIA.csv
diff --git a/...s/lung_cancer_cptac_DataExploration.ipynb → ...d/lung_cancer_cptac_DataExploration.ipynb b/...s/lung_cancer_cptac_DataExploration.ipynb → ...d/lung_cancer_cptac_DataExploration.ipynb
diff --git a/notebooks/pathomics/README.md b/notebooks/pathomics/README.md
@@ -1,7 +1,7 @@
 # Introduction to working with digital pathology images in IDC
-This repository contains a short notebook (lung_cancer_cptac_DataExploration.ipynb) giving an idea on how to explore available collections of pathology whole-slide images (WSIs) in the IDC. 
+This repository contains a short notebook (getting_started_with_digital_pathology.ipynb) giving an idea on how to explore and work with available collections of pathology whole-slide images (WSIs) in the IDC. 
 
-More elaborate tutorials on how to train a tissue classification model can be found in the Github repository [idc-comppath-reproducibility](https://github.com/ImagingDataCommons/idc-comppath-reproducibility) as part of the publication below:
+More tutorials that show, for example, how to train a tissue classification model can be found in the Github repository [idc-comppath-reproducibility](https://github.com/ImagingDataCommons/idc-comppath-reproducibility) as part of the publication below:
 
 > Schacherer, D. P., Herrmann, M. D., Clunie, D. A., Höfener, H., Clifford, W., Longabaugh, W. J. R., Pieper, S., Kikinis, R., Fedorov, A. & Homeyer, A. The NCI Imaging Data Commons as a platform for reproducible research in computational pathology. _Computer Methods and Programs in Biomedicine_. 107839 (2023). [doi:10.1016/j.cmpb.2023.107839](https://doi.org/10.1016/j.cmpb.2023.107839)
 

diff --git a/notebooks/pathomics/getting_started_with_digital_pathology.ipynb b/notebooks/pathomics/getting_started_with_digital_pathology.ipynb